Dev

build.gradle

@@ -14,6 +14,11 @@ plugins {
 repositories {
     mavenCentral()
     mavenLocal()
+    maven {
+        name = "sonatypeSnapshots"
+        url = uri("https://central.sonatype.com/repository/maven-snapshots/")
+        mavenContent { snapshotsOnly() }
+    }
 }
 
 import org.apache.tools.ant.filters.ReplaceTokens
@@ -95,7 +100,7 @@ dependencies {
             [group: 'org.apache.commons', name: 'commons-compress', version: '1.26.0'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.18.0'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '4.3.0'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '5.0.0'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'],
             [group: 'com.google.guava', name: 'guava', version: '32.1.3-jre'],

src/main/java/org/igv/batch/CommandExecutor.java

@@ -200,14 +200,16 @@ public String execute(String commandLine) throws IOException {
             HttpUtils.getInstance().clearAccessTokens();
         } else if (cmd.equalsIgnoreCase("sortByAttribute")) {
             result = sortByAttribute(args);
-        } else if (cmd.equalsIgnoreCase("fitTracks")) {
-            igv.fitTracksToPanel();
+        } else if (cmd.equalsIgnoreCase("fitTracks") || cmd.equals("minimizeTrackHeights")) {
+            igv.minimizeTrackHeights();
         } else if (cmd.equalsIgnoreCase("showAttributes")) {
             result = this.showAttributes(args);
         } else if (cmd.equalsIgnoreCase("showDataRange")) {
             result = this.setShowDataRange(param1, param2);
         } else if (cmd.equalsIgnoreCase("setTrackHeight")) {
             result = this.setTrackHeight(param1, param2);
+        } else if (cmd.equalsIgnoreCase("setRowHeight")) {
+            result = this.setRowHeight(param1, param2);
         } else if (cmd.equalsIgnoreCase("overlay")) {
             result = this.overlay(args);
         } else if (cmd.equalsIgnoreCase("separate")) {
@@ -539,6 +541,31 @@ private String setTrackHeight(String param1, String param2) {
         }
     }
 
+    private String setRowHeight(String param1, String param2) {
+
+        int height;
+        String trackName;
+        try {
+            height = Integer.parseInt(param1);
+            trackName = parseTrackName(param2);
+        } catch (NumberFormatException e) {
+            height = Integer.parseInt(param2);
+            trackName = parseTrackName(param1);
+        }
+
+        height = Math.max(0, height);
+        List<Track> tracks = tracksMatchingName(trackName);
+        if (tracks.size() > 0) {
+            for (Track track : tracks) {
+                track.setRowHeight(height);
+            }
+            igv.repaint();
+            return "OK";
+        } else {
+            return String.format("Error: Track %s not found", trackName);
+        }
+    }
+
     private String setShowDataRange(String show, String trackName) {
 
         boolean showDataRange;

src/main/java/org/igv/event/TrackSelectionEvent.java

@@ -0,0 +1,7 @@
+package org.igv.event;
+
+/**
+ * Posted when a track's selection checkbox is toggled.
+ */
+public final class TrackSelectionEvent implements IGVEvent {
+}

src/main/java/org/igv/feature/EmblFeatureTableParser.java

@@ -50,7 +50,6 @@ public List<FeatureTrack> loadTracks(ResourceLocator locator, Genome genome) {
             } else {
                 FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
                 track.setName(locator.getTrackName());
-                track.setMinimumHeight(35);
                 track.setHeight(45);
                 track.setRenderer(new GeneTrackRenderer());
 

src/main/java/org/igv/feature/genome/load/DotGenomeLoader.java

@@ -61,8 +61,6 @@ private static FeatureTrack createGeneTrack(Genome genome, BufferedReader reader
 
                 String id = genome.getId() + "_genes";
                 geneFeatureTrack = new FeatureTrack(id, name, new FeatureCollectionSource(genes, genome));
-                geneFeatureTrack.setMinimumHeight(5);
-                geneFeatureTrack.setHeight(35);
                 geneFeatureTrack.setDataType(DataType.GENE);
                 TrackProperties props = parser.getTrackProperties();
                 if (props != null) {

src/main/java/org/igv/feature/genome/load/GenomeLoader.java

@@ -68,7 +68,9 @@ public static GenomeLoader getLoader(String genomePath) throws IOException {
 
 
     /**
-     * Create an annotation track for the genome from a supplied list of features
+     * Create an annotation track for the genome from a supplied list of features.
+     *
+     * This is used by the ".genome" and genbank loaders, which include annotations within the genome file.
      *
      * @param genome
      * @param features
@@ -81,8 +83,6 @@ public static FeatureTrack createGeneTrack(Genome genome, List<htsjdk.tribble.Fe
 
         String id = genome.getId() + "_genes";
         geneFeatureTrack = new FeatureTrack(id, name, new FeatureCollectionSource(features, genome));
-        geneFeatureTrack.setMinimumHeight(5);
-        geneFeatureTrack.setHeight(35);
 
         return geneFeatureTrack;
     }

src/main/java/org/igv/prefs/Constants.java

@@ -87,6 +87,7 @@ private Constants() {
     public static final String CHART_SHOW_ALL_HEATMAP = "CHART.SHOW_ALL_HEATMAP";
     public static final String SHOW_REGION_BARS = "SHOW_REGION_BARS";
     public static final String DEFAULT_VISIBILITY_WINDOW = "DEFAULT_VISIBILITY_WINDOW";
+    public static final String FIT_TO_VIEWPORT_MAX_ROWS = "FIT_TO_VIEWPORT_MAX_ROWS";
     public static final String EXPAND_FEAUTRE_TRACKS = "EXPAND_FEATURE_TRACKS";
     public static final String IGV_PLUGIN_LIST_KEY = "IGV_PLUGIN_LIST";
     public static final String SASHIMI_SHOW_COVERAGE = "SASHIMI.SHOW_COVERAGE";

src/main/java/org/igv/renderer/DataRenderer.java

@@ -35,6 +35,11 @@ public abstract class DataRenderer implements Renderer<LocusScore> {
     protected static final int AXIS_AREA_WIDTH = 60;
     protected static Color axisLineColor = new Color(255, 180, 180);
 
+
+    public int getMinimumHeight() {
+        return 20;
+    }
+
     /**
      * Render the track in the given rectangle.
      *
@@ -54,7 +59,6 @@ public void render(List<LocusScore> scores, RenderContext context, Rectangle rec
             }
         }
         renderGuides(track, context, rect);
-
     }
 
     /**

src/main/java/org/igv/renderer/HeatmapRenderer.java

@@ -20,8 +20,9 @@ public class HeatmapRenderer extends DataRenderer {
 
     private static Logger log = LogManager.getLogger(HeatmapRenderer.class);
 
-    public String getDisplayName() {
-        return "Heatmap";
+    @Override
+    public int getMinimumHeight() {
+        return 1;
     }
 
     /**

src/main/java/org/igv/renderer/IGVFeatureRenderer.java

@@ -32,9 +32,10 @@ public class IGVFeatureRenderer extends FeatureRenderer {
     static protected final int REGION_STRAND_THICKNESS = 4;
     static final int BLOCK_HEIGHT = 14;
     static final int THIN_BLOCK_HEIGHT = 6;
+    static final int NON_CODING_HEIGHT = 8;
     protected Color AA_COLOR_1 = new Color(92, 92, 164);
     protected Color AA_COLOR_2 = new Color(12, 12, 120);
-    static final int NON_CODING_HEIGHT = 8;
+
 
     private static final Color VARIANT_HET_COLOR = Color.blue.brighter();
     private static final Color VARIANT_HOM_COLOR = new Color(0, 245, 255);
@@ -49,13 +50,9 @@ public class IGVFeatureRenderer extends FeatureRenderer {
     //protected double lastRegionMaxY = 0;
 
 
-    int blockHeight = BLOCK_HEIGHT;
-    int thinBlockHeight = THIN_BLOCK_HEIGHT;
-
-    //Map from Exon to y offset
-    //Could use more coordinates, but they are all contained in the Exon
-    private Map<IExon, Integer> exonMap = new HashMap<IExon, Integer>(100);
-    private Set<String> drawnNames = new HashSet<String>(100);
+    transient int blockHeight ;
+    transient int thinBlockHeight;
+    transient int nonCodingHeight ;
 
     protected boolean isGenotypeRenderer = false;
 
@@ -85,9 +82,10 @@ public void render(List<IGVFeature> featureList,
         double locScale = context.getScale();
         double end = origin + trackRectangle.getWidth() * locScale;
 
-        final Track.DisplayMode displayMode = track.getDisplayMode();
-        blockHeight = displayMode == Track.DisplayMode.SQUISHED ? BLOCK_HEIGHT / 2 : BLOCK_HEIGHT;
-        thinBlockHeight = displayMode == Track.DisplayMode.SQUISHED ? THIN_BLOCK_HEIGHT / 2 : THIN_BLOCK_HEIGHT;
+        final int rowHeight = Math.max(1, track.getRowHeight());
+        blockHeight = Math.min(BLOCK_HEIGHT, rowHeight / 2);
+        thinBlockHeight = Math.min( THIN_BLOCK_HEIGHT, blockHeight / 2);
+        nonCodingHeight = Math.min(thinBlockHeight, NON_CODING_HEIGHT);
 
         if ((featureList != null) && (featureList.size() > 0)) {
 
@@ -188,18 +186,18 @@ public void render(List<IGVFeature> featureList,
                     if ((pixelWidth < 3)) {
                         drawFeatureBounds(pixelStart, pixelEnd, pixelYCenter, g2D);
                     } else {
-                        drawExons(feature, pixelYCenter, context, g2D, trackRectangle, displayMode,
+                        drawExons(feature, pixelYCenter, context, g2D, trackRectangle, rowHeight,
                                 alternateExonColor, track.getColor(), track.getAltColor());
                     }
                 } else {
 
                     // If there is room create a gap between this feature and the next
                     drawFeatureBlock(pixelStart, pixelEnd, pixelThickStart, pixelThickEnd, pixelYCenter, g2D);
 
-                    if (displayMode != Track.DisplayMode.SQUISHED) {
+                    if (rowHeight >= 5) {
                         Graphics2D arrowGraphics = context.getGraphic2DForColor(Color.WHITE);
                         drawStrandArrows(feature.getStrand(), pixelStart, pixelEnd, pixelYCenter, 0,
-                                displayMode, trackRectangle, arrowGraphics);
+                                rowHeight, trackRectangle, arrowGraphics);
                     }
 
                     // This is ugly, but alternatives are probably worse
@@ -223,7 +221,7 @@ public void render(List<IGVFeature> featureList,
 
 
                 // Draw name , if there is room
-                if (displayMode != Track.DisplayMode.SQUISHED && track.isShowFeatureNames()) {
+                if (rowHeight >= 10 && track.isShowFeatureNames()) {
 
                     String name = labelField != null ? feature.getDisplayName(labelField) : feature.getName();
 
@@ -247,7 +245,7 @@ public void render(List<IGVFeature> featureList,
                         // Calculate the minimum amount of vertical track
                         // space required be we  draw the
                         // track name without drawing over the features
-                        int verticalSpaceRequiredForText = textBaselineY - (int) trackRectangleY;
+                        int verticalSpaceRequiredForText = fontHeight + blockHeight + 5;
 
                         if (verticalSpaceRequiredForText <= trackRectangle.height) {
                             lastNamePixelEnd = drawFeatureName(name, track.getDisplayMode(), nameStart, nameEnd,
@@ -339,7 +337,7 @@ private void drawFeatureBounds(int pixelStart, int pixelEnd, int yOffset, Graphi
     }
 
     protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
-                             Graphics2D g2D, Rectangle trackRectangle, Track.DisplayMode mode,
+                             Graphics2D g2D, Rectangle trackRectangle, int rowHeight,
                              boolean alternateExonColor, Color color1, Color color2) {
 
         // Now get the individual regions of the
@@ -420,7 +418,7 @@ protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                     && lastExonEndX >= maxLineEndX) {
                 drawConnectingLine(lastExonEndX, lastY, pStart, curYOffset, exon.getStrand(), blockGraphics);
                 double angle = Math.atan(-(curYOffset - lastY) / ((pStart - lastExonEndX) + 1e-12));
-                drawStrandArrows(gene.getStrand(), lastExonEndX, pStart, lastY, angle, mode, trackRectangle, blockGraphics);
+                drawStrandArrows(gene.getStrand(), lastExonEndX, pStart, lastY, angle, rowHeight, trackRectangle, blockGraphics);
                 maxLineEndX = Math.max(maxLineEndX, pStart);
             }
             lastExonEndX = pEnd;
@@ -444,9 +442,9 @@ protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                             blockGraphics,
                             exon,
                             pClippedStart,
-                            curYOffset - NON_CODING_HEIGHT / 2,
+                            curYOffset - nonCodingHeight / 2,
                             pClippedWidth,
-                            NON_CODING_HEIGHT);
+                            nonCodingHeight);
 
                 } else {
                     // Exon contains 5' UTR -- draw non-coding part
@@ -458,9 +456,9 @@ protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                                 blockGraphics,
                                 exon,
                                 pClippedStart,
-                                curYOffset - NON_CODING_HEIGHT / 2,
+                                curYOffset - nonCodingHeight / 2,
                                 pClippedWidth,
-                                NON_CODING_HEIGHT);
+                                nonCodingHeight);
                         pStart = pCdStart;
                     }
                     //  Exon contains 3' UTR  -- draw non-coding part
@@ -472,8 +470,8 @@ protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                                 blockGraphics,
                                 exon,
                                 pClippedStart,
-                                curYOffset - NON_CODING_HEIGHT / 2,
-                                pClippedWidth, NON_CODING_HEIGHT);
+                                curYOffset - nonCodingHeight / 2,
+                                pClippedWidth, nonCodingHeight);
                         pEnd = pCdEnd;
                     }
                     // At least part of this exon is coding.  Draw the coding part.
@@ -486,10 +484,10 @@ protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                 }
 
                 Graphics2D whiteArrowGraphics = context.getGraphic2DForColor(Color.white);
-                drawStrandArrows(gene.getStrand(), pStart + ARROW_SPACING / 2, pEnd, curYOffset, 0, mode,
+                drawStrandArrows(gene.getStrand(), pStart + ARROW_SPACING / 2, pEnd, curYOffset, 0, rowHeight,
                         trackRectangle, whiteArrowGraphics);
 
-                if (locationScale < 0.25) {
+                if (locationScale < 0.25 && rowHeight > 10) {
                     labelAminoAcids(pStart, fontGraphics, theOrigin, context, gene, locationScale,
                             curYOffset, trackRectangle, idx);
                 }
@@ -518,15 +516,15 @@ protected void drawExonRect(Graphics blockGraphics, Exon exon, int x, int y, int
      * @param endX
      * @param startY
      * @param angle
-     * @param mode
+     * @param rowHeight
      * @param g2D
      */
     protected void drawStrandArrows(Strand strand,
                                     int startX,
                                     int endX,
                                     int startY,
                                     double angle,
-                                    Track.DisplayMode mode,
+                                    int rowHeight,
                                     Rectangle trackRectangle,
                                     Graphics2D g2D) {
 
@@ -546,7 +544,7 @@ protected void drawStrandArrows(Strand strand,
 
 
         // Draw the directional arrows on the feature
-        int sz = mode == Track.DisplayMode.EXPANDED ? 3 : 2;
+        int sz = rowHeight < 5 ?  2 : 3;
         sz = strand.equals(Strand.POSITIVE) ? -sz : sz;
         final int asz = Math.abs(sz);
 
@@ -594,8 +592,6 @@ final private int drawFeatureName(String name,
             // g2D.clearRect(xString2, textBaselineY, (int) stringBounds.getWidth(), (int) stringBounds.getHeight());
             g2D.drawString(name, nameStart, textBaselineY);
             lastFeatureEndedAtPixelX = nameStart + nameWidth;
-            drawnNames.add(name);
-
         }
 
         return lastFeatureEndedAtPixelX;
@@ -695,9 +691,4 @@ protected int getPixelFromChromosomeLocation(String chr, int chromosomeLocation,
         return (int) Math.round((chromosomeLocation - origin) / locationScale);
     }
 
-    @Override
-    public void reset() {
-        exonMap.clear();
-        drawnNames.clear();
-    }
 }

src/main/java/org/igv/sam/AlignmentRenderer.java

@@ -306,7 +306,7 @@ public void renderAlignments(List<Alignment> alignments,
                 // Does the change for Bisulfite kill some machines?
                 double pixelWidth = pixelEnd - pixelStart;
                 Color alignmentColor = getAlignmentColor(alignment, track);
-                final boolean leaveMargin = (this.track.getDisplayMode() != Track.DisplayMode.SQUISHED);
+                final boolean leaveMargin = (this.track.getRowHeight() > 2);
                 final ColorOption colorOption = renderOptions.getColorOption();
                 if ((pixelWidth < 2) &&
                         !((AlignmentTrack.isBisulfiteColorType(colorOption) ||
@@ -976,6 +976,7 @@ private void drawAlignment(
 
     /**
      * get a texture to apply to duplicate reads, caches the created textures according to their color
+     *
      * @param baseColor the color to render the read
      * @return a texture matching the base color with shading
      */
@@ -1158,7 +1159,7 @@ private Color getAlignmentColor(Alignment alignment, AlignmentTrack track) {
         // Set color used to draw the feature.  Highlight features that intersect the
         // center line.  Also restorePersistentState row "score" if alignment intersects center line
 
-        Color defaultColor = track.getColor();
+        Color defaultColor = alignment.isNegativeStrand()  ? track.getAltColor() : track.getColor();
         Color c = defaultColor;
         AlignmentTrack.RenderOptions renderOptions = track.getRenderOptions();
         ColorOption colorOption = renderOptions.getColorOption();